AffiXcan-package {AffiXcan} | R Documentation

## A functional approach to impute GReX

### Description

Impute a GReX (Genetically Regulated Expression) for a set of genes in a sample of individuals, using a method based on the Total Binding Affinity (TBA) score. Statistical models to impute GReX can be trained on a training dataset where the real total expression values are known.

### Details

For every gene a linear regression model can be fitted on a training set of individuals where the real total expression values, the Total Binding Affinity (TBA) values for a set of genomic regions, and the covariates of the population genetic structure, are known. AffiXcan performs a principal component analysis (PCA) on the TBA values to fit a linear model using the formula: GReX ~ PC1 + PC2 + PC3 + ... + COV1 + COV2 + ... . Associations between the expressed genes and the regulatory regions, on which the TBA values have to be computed, are needed. TBA can be computed using "vcf_rider" software (see references)

### Author(s)

Alessandro Lussana <alessandro.lussana@protonmail.com> Maintainer: Alessandro Lussana <alessandro.lussana@protonmail.com>

### References

https://github.com/vodkatad/vcf_rider

### Examples

    trainingTbaPaths <- system.file("extdata","training.tba.toydata.rds",
    package="AffiXcan")

    data(exprMatrix)
    data(regionAssoc)
    data(trainingCovariates)

    assay <- "values"

    training <- affiXcanTrain(exprMatrix=exprMatrix, assay=assay,
    tbaPaths=trainingTbaPaths, regionAssoc=regionAssoc, cov=trainingCovariates,
    varExplained=80, scale=TRUE)

    testingTbaPaths <- system.file("extdata","testing.tba.toydata.rds",
    package="AffiXcan")

    exprmatrix <- affiXcanImpute(tbaPaths=testingTbaPaths, affiXcanTraining=training,
    scale=TRUE)

[Package AffiXcan version 1.10.0 Index]